Introduction to Organic Geochemistry E-Book

Stephen D. Killops

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 1027

Veröffentlichungsjahr: 2013

Beschreibung

An Introduction to Organic Geochemistry explores the fate of organic matter of all types, biogenic and man-made, in the Earth System.

• investigates the variety of pathways and biogeochemical transformations that carbon compounds can experience over a range of time scales and in different environments
  
• scope widened to provide a broad and up-to-date background - structured to accommodate readers with varied scientific backgrounds
  
• essential terminology is defined fully and boxes are used to explain concepts introduced from other disciplines
  
• further study aided by the incorporation of carefully selected literature references
  
• It investigates the variety of pathways and biogeochemical transformations that carbon compounds can experience over a range of time scales and in different environments.

Leseprobe

Contents

Preface

Acknowledgements

1 Carbon, the Earth and life

1.1 Carbon and the basic requirements of life

1.2 Chemical elements, simple compounds and their origins

1.3 The origin of life

1.4 Evolution of life and the atmosphere

1.5 Major contributors to sedimentary organic matter

2 Chemical composition of organic matter

2.1 Structure of natural products

2.2 Carbohydrates

2.3 Amino acids and proteins

2.4 Lipids

2.5 Lignins, tannins and related compounds

2.6 Nucleotides and nucleic acids

2.7 Geochemical implications of compositional variation

3 Production, preservation and degradation of organic matter

3.1 How and why organic-rich deposits form

3.2 Controls on primary production

3.3 Preservation and degradation of organic matter

3.4 Depositional environments associated with accumulation of organic matter

4 Long-term fate of organic matter in the geosphere

4.1 Diagenesis

4.2 Humic material

4.3 Coal

4.4 Kerogen

4.5 Catagenesis and metagenesis

4.6 Temporal and geographical distribution of fossil organic carbon

5 Chemical stratigraphic concepts and tools

5.1 Biologically mediated transformations

5.2 Examples of source indicators in Recent sediments

5.3 Diagenesis at the molecular level

5.4 Source and environmental indicators in ancient sediments and oil

5.5 Thermal maturity and molecular transformations

5.6 Palaeotemperature and age measurement

5.7 Maturity of ancient sedimentary organic matter

5.8 Isotopic palaeontology

6 The carbon cycle and climate

6.1 Global carbon cycle

6.2 Changes in carbon reservoirs over geological time

6.3 Palaeoclimatic variations

6.4 Isotopic excursions at period boundaries

6.5 Human influence on the carbon cycle

7 Anthropogenic carbon and the environment

7.1 Introduction

7.2 Halocarbons

7.3 Hydrocarbon pollution in aquatic environments

7.4 Endocrine-disrupting chemicals

7.5 Environmental behaviour of selected xenobiotic compounds

7.6 Factors affecting the fate of anthropogenic components

Appendix 1 SI units used in this book

Appendix 2 SI unit prefixes

Appendix 3 Geological time scale

References

Index

© 2005 Blackwell Science Ltd, a Blackwell Publishing company

BLACKWELL PUBLISHING

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The right of Stephen Killops and Vanessa Killops to be identified as the Authors of this Work has been asserted in accordance with the UK Copyright, Designs, and Patents Act 1988.

All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, except as permitted by the UK Copyright, Designs, and Patents Act 1988, without the prior permission of the publisher.

First edition published 1993 by Longman Scientific and Technical

Second edition published 2005 by Blackwell Publishing Ltd

Library of Congress Cataloging-in-Publication Data

Killops, S.D. (Stephen Douglas), 1953–

Introduction to organic geochemistry / Stephen Killops and Vanessa Killops.–2nd ed.

p. cm.

Includes bibliographical references and index.

ISBN 0-632-06504-4 (pbk. : alk. paper)

1. Organic geochemistry. I. Killops, V. J. (Vanessa Jane), 1955– II. Title.

QE516.5K55 2005

553.2–dc22

2004003107

A catalogue record for this title is available from the British Library.

For further information on

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Preface

To begin with, a brief statement of what constitutes organic geochemistry is probably called for. It is the study of the transformation undergone by organic matter of all types, whether of biological or manmade origin, in the Earth System. The transformations involved vary from those mediated by biological processes involved in the production of living tissue and the operation of food-chains, to those controlled by temperature and pressure at depth in the crust. Photochemical processes in the atmosphere and hydrosphere can also be important in controlling the environmental behaviour of some organic compounds.

Our knowledge of organic geochemistry has been expanding at such a great rate that a comprehensive text on the subject would fill many books of this size. To a newcomer, the bulk of information and the terminology adopted from a range of disciplines, such as chemistry, geology, ecology, biochemistry, botany and oceanography, can be quite daunting. However, to those not readily deterred, the fascination of the subject soon becomes apparent. If only the basics of organic geochemistry could be found readily at hand rather than scattered through textbooks and journals of a number of disciplines! These were our thoughts when we first came to the subject in the 1980s, and they subsequently provided the stimulus for this book when one of us (SDK) began teaching the subject to undergraduates and postgraduates.

This book is an attempt to present a readily accessible, up-to-date and integrated introduction to organic geochemistry, at a reasonable price. It does not assume any particular specialist knowledge, and explanatory boxes are used to provide essential information about a topic or technique. Technical terms are also highlighted and explained at their first appearance in the text.SI units are presented in Appendix 1, prefixes used to denote exponents in Appendix 2 and a geological time scale in Appendix 3. A comprehensive reference list is provided for those wishing to explore the original sources of the concepts and case studies covered, which concentrates on articles in the most readily available journals.

The text is intended to serve undergraduate and postgraduate courses in which organic geochemistry is an important component. It may also be found a useful companion by experienced scientists from other disciplines who may be moving into the subject for the first time. Whereas the first edition of this book concentrated on organic-rich deposits, of particular interest to those involved in petroleum exploration, this edition considers the fate of organic matter in general. The importance of environmental geochemistry has not been overlooked, and consideration has been given to environmental change at various times during Earth’s history in order to provide a background for assessing modern changes and how the carbon cycle works. Naturally, in a book of this size it is impossible to cover everything;for example, it is not possible to do justice to the wide range of analytical techniques used in organic geochemistry, which draw on all aspects of separation science and spectrometry. However, there are many texts on these topics, some of which are listed below. We hope the topics we have selected for this edition stimulate the reader to continue studying organic geochemistry.

Further reading

Harwood L.M., Claridge T.D.W. (1997) Introduction to Organic Spectroscopy. Oxford: Oxford Science Publications.

Lewis C.A. (1997) Analytical techniques in organic chemistry. In Modern Analytical Geochemistry (ed. Gill R.), 243–72. Harlow: Longman.

Peters K.E., Moldowan J.M.(1993) The Biomarker Guide: Interpreting Molecular Fossils in Petroleum and Ancient Sediments. Englewood Cliffs, NJ: Prentice Hall.

Poole C. (2002) The Essence of Chromatography. Amsterdam: Elsevier Health Sciences.

Settle F. (ed.) (1997) Instrumental Techniques for Analytical Chemistry. Englewood Cliffs, NJ: Prentice Hall.

Silverstein R.M., Bassler C.G., Morrill T.C. (1991) Spectrometric Identification of Organic Compounds. New York: Wiley.

Acknowledgements

The authors wish to thank their colleagues, for advice and helpful comments during the preparation of this book, and the library at Plymouth University. We are particularly grateful to those who volunteered their time and expertise in reviewing the manuscript: Dr Geoff Abbott (NRG in Fossil Fuels and Environmental Geochemistry, University of Newcastle-upon-Tyne); Prof. Carrine Blank (Dept of Earth and Planetary Sciences, Washington University); Dr Paul Finch (Centre for Chemical Science, Royal Holloway, University of London); Prof. Andy Fleet (Dept of Mineralogy, Natural History Museum, London); Dr Anthony Lewis (School of Environmental Sciences, Plymouth University); Dr Dave McKirdy (School of Earth and Environmental Sciences, University of Adelaide); Prof. Phil Meyers (Dept of Geological Sciences, University of Michigan); Dr Fred Prahl (College of Oceanic and Atmospheric Sciences, Oregon State University);Dr Lloyd Snowdon (Geological Survey of Canada, Calgary).

1

Carbon, the Earth and life

1.1 Carbon and the basic requirements of life

In its broadest sense, organic geochemistry concerns the fate of carbon, in all its variety of chemical forms, in the Earth system. Although one major form of carbon is strictly inorganic, carbon dioxide, it is readily converted by photosynthesis into the stuff of life, organic compounds (see Box 1.9), and so must be included in our consideration of organic geochemistry. From chiefly biological origins, organic compounds can be incorporated into sedimentary rocks (Box 1.1) and preserved for tens of millions of years, but they are ultimately returned to the Earth’s surface, by either natural processes or human action, where they can participate again in biological systems. This cycle involves various biochemical and geochemical transformations, which form the central part of the following account of organic geochemistry. To understand these transformations and the types of organic compounds involved we must first consider the origins and evolution of life and the role played by carbon.

Growth and reproduction are among the most obvious characteristics of life, and require the basic chemicals from which to build new cellular material, some form of energy to drive the processes and a means of harnessing and distributing this energy. There is an immense range of compounds involved in these processes. For example, energy is potentially dangerous; the sudden release of the energy available from complete oxidation of a single molecule of glucose is large when considered at a cellular level. Therefore, a range of compounds is involved in bringing about this reaction safely by a sequence of partial oxidations, and in the storage and transport to other sites in the cell of the more moderate amounts of energy released at each step. We look at the geochemically important compounds involved in life processes in Chapter 2.

What makes carbon such an important element is its ability to form an immense variety of compounds—primarily with the elements hydrogen, oxygen, sulphur and nitrogen, as far as natural products are concerned—with an equally wide range of properties; this is unparalleled by other elements. This variety of properties allows carbon compounds to play the major role in the creation and maintenance of life. The strength of the chemical bonds in organic compounds is sufficiently high to permit stability, which is essential in supportive tissue, for example, but low enough not to impose prohibitive energy costs to an organism in synthesizing and transforming compounds.

Box 1.1 Sediments and sedimentary rocks

Sediment is the solid material, inorganic or organic, that settles out of suspension from a fluid phase (normally water, ice or air) in which it has been transported. Over time, under the right conditions, it can undergo lithification (i.e. conversion into a solid body of rock). Various processes can be involved in lithification: compaction, cementation, crystallization and desiccation.

Inorganic sediment is supplied by erosion of material from exposed areas of high relief, and can be transported a considerable distance to the area of deposition. The composition of this detrital (or clastic) material varies, but aluminosilicate minerals are usually important. There are also biogenic sediments, resulting from the remains of organisms (e.g. calcareous and siliceous tests, peat) and chemical sediments formed by precipitation of minerals from solution (e.g. evaporites, some limestones and authigenic infills of pores by quartz and calcite cements).

The nature of the sediments accumulating in a particular location can change over time, allowing the recognition of different bodies of sedimentary rock. Such a body is termed a facies, and it displays a set of characteristic attributes that distinguish it from vertically adjacent bodies. Various distinguishing attributes include sedimentary structures, mineral content and fossil assemblages. Organofacies can also be recognized, based on compositional differences in the organic material present (Jones 1987; Tyson 1995).

Another prerequisite for life is liquid water, the medium in which biochemical reactions take place and usually the main constituent of organisms. Although bacteria, and even some simple animals, like the tardigrade, can survive in a dormant state without water, the processes that we associate with life can only take place in its presence. This requirement obviously imposes temperature limits on environments that can be considered suitable for life; hence one of the criteria in the search for life on other planets is evidence for the existence of liquid water at some stage of a planet’s life.

1.2 Chemical elements, simple compounds and their origins

1.2.1 Origin of elements

Carbon is the twelfth most abundant element in the Earth’s crust, although it accounts for only c.0.08% of the combined lithosphere (see Box 1.2), hydrosphere and atmosphere. Carbon-rich deposits are of great importance to humans, and comprise diamond and graphite (the native forms of carbon), calcium and magnesium carbonates (calcite, limestone, dolomite, marble and chalk) and fossil fuels (gas, oil and coal). Most of these deposits are formed in sedimentary environments, although the native forms of C require high temperature and pressure, associated with deep burial and metamorphism.

Where did the carbon come from? The universe is primarily composed of hydrogen, with lesser amounts of helium, and comparatively little of the heavier elements (which are collectively termed metals by astronomers). The synthesis of elements from the primordial hydrogen, which was formed from the fundamental particles upon the initial stages of cooling after the Big Bang some 15 Gyr ago, is accomplished by nuclear fusion, which requires the high temperatures and pressures within the cores of stars. Our Sun is relatively small in stellar terms, with a mass of c.2 × 1030 kg, and is capable of hydrogen fusion, which involves the following reactions:

[Eqn 1.1]

[Eqn 1.2]

[Eqn 1.3]

(where 2H can also be written as D, or deuterium, and the superscript numbers represent the mass numbers as described in Box 1.3). Because of the extremely high temperatures and pressures, electrons are stripped off atoms to form a plasma and it is the remaining nuclei that undergo fusion reactions. Ultimately, when enough helium has been produced, helium fusion can then begin. This process is just possible in stars of the mass of our Sun, and results in the creation of carbon first and then oxygen:

[Eqn 1.4]

[Eqn 1.5]

Box 1.2 Earth’s structure

Temperature and pressure both increase with depth in the Earth and control the composition and properties of the material present at various depths. The Earth comprises a number of layers, the boundaries between which are marked by relatively abrupt compositional and density changes (Fig. 1.1). The inner core is an iron–nickel alloy, which is solid under the prevailing pressure and temperature ranges. In contrast, the outer core is molten and comprises an iron alloy, the convection currents within which are believed to drive the Earth’s magnetic field. The core–mantle boundary lies at 2900km depth and marks the transition to rocky material above. The can be divided into upper and lower parts, although the boundary is quite a broad transitional zone (.1000–400km depth). It behaves in a plastic, ductile fashion and supports convection cells. The upper mantle layer from .100 to 400km depth is called the , and its convection system carries the drifting continental plates.